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  • Can MAQ be used for 454 sequencing data for SNP detection?

    hello,


    I am having 454 sequencing data from which i am trying to find SNPs. Can MAQ do that thing for me, I know that it is mostly used for SOLEXA sequence reads, but anyone have ever tried with 454 sequencing data?

    If yes, whether results are reliable?

    Which from following softwares i choose, MAQ/MOSAIK/SAMtools?

    Thanks.

  • #2
    Perhaps try Mosaik, Roche's GsAssembler, or Novoalign for alignment
    then Samtools / Varscan for variant calling.

    Maq is not appropriate for 454 in my experience

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    • #3
      I haven't tried it on 454 data (yet! perhaps today!) but the BWA package contains a mode (bwasw) for handling long reads.

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      • #4
        Careful, from the bwa site:

        Does BWA align 454 reads?

        Yes and no. The BWA-SW component of BWA works well on 454 reads about 200bp or longer. It achieves similar alignment accuracy to SSAHA2 while much faster. BWA-SW also works for shorter reads, but the sensitivity is lower. In addition, BWA-SW does not support paired-end alignment.
        -drd

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        • #5
          My strong recommendation is to use Roche's gsMapper (part of Newbler) for aligning 454 reads to a reference. It has specific handling for the 454 error model (homopolymeric tract errors, indels) which other aligners may not have.

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          • #6
            Thank you for your reply.
            Right now i am trying with MOSAIK.

            Which program should i use to convert sff to fasq, self_extract.py then fastaqual2fastq.pl or indraneil's sff2fastq?

            Thanks

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